Research & Publications
My research is focused on understanding the molecular basis of a variety of lung disease ranging from asthma to lung cancer. I study the role of a recently discovered group of genes called non-coding RNAs (ncRNAs). These molecules are expressed in the cells, but rather than coding a specific protein, target and modify the expression of other RNAs including messenger RNAs (mRNAs).
In our workflow we first measure the levels of coding and non-coding RNAs in human samples and animal models to identify changes in ncRNAs and candidate target genes that are unique to a specific lung pathology. We then analyze the relationship between these regulatory elements through various bioinformatic and biochemical methods. Finally, we directly investigate the role of these ncRNAs and their targets by modulating their expression in disease models and testing their effects on specific pathogenic mechanisms.
One of our main research interests in recent years has been the role of ncRNAs in the lung endothelium. We are trying to answer questions such as how and why vascular cells become injured or inflamed in diseases like asthma and ARDS, and how activation of these cells permits the survival and propagation of cancerous cells in the lung. In continuation of our research, we are focusing on cellular enzymes that modify non-coding RNAs, and in particular microRNAs. Another focus of our research is the interaction of immune cells and platelets with the endothelium and the role of non-coding RNAs in defining these interactions.
Extensive Research Description
The overall goal of my research program is to determine the role of non-coding RNAs in the lung pathologies. My background is in basic molecular biology with a focus on RNA biochemistry and structural biology. We have established the basic experimental tools necessary for the identification and modulation of expression of non-coding RNAs in various cellular compartments of the lung.
Our projects are focused in three major areas:
1. The Role of Endothelial Non-coding RNAS in Lung Inflammation and Cancer
We have shown that miR-1 regulation plays a critical role in determining the endothelial response in lung inflammation and tumor progression. We have also shown that miR-1 targets Mpl in the lung endothelium and modulates the expression of adhesion molecules and recruitment of inflammatory cells into the lung. We have developed an endothelial-specific miR-1 expression lentiviral vector and an inducible endothelial-specific miR-1 transgenic mouse, validated the efficiency and specificity of these models and used them in studies on type 2 inflammation and NSCLC tumor progression and angiogenesis. We have found that endothelial miR-1 also plays a protective role in the lung and modulates “angiocrine signaling” between endothelium and epithelial compartments. Our publications in this area include:
- I.Takyar S, Vasavada H, Zhang JG, Ahangari F, Niu N, Liu Q, Lee CG, Cohn L, Elias JA. VEGF controls lung Th2 inflammation via the miR-1-Mpl (myeloproliferative leukemia virus oncogene)-P-selectin axis. J Exp Med 2013; 210: 1993-2010. PMID:24043765
- II.Haslip M, Jin L, Siegel I, Takyar S. Endothelial MicroRNA-1 Protects Against Lung Hyperoxic Injury and Downregulates Ang2 Expression, B57. Gene Regulation: miRNAs and epigenetics, American Thoracic Society; May 1, 2015, A3487-A3487
- Korde, A., Jin, L., Zhang, J. G., Ramaswamy, A., Hu, B., Kolahian, S., Juan Guardela, B., Herazo-Maya, J., Siegfried, J. M., Stabile, L., Pisani, M. A., Herbst, R. S., Kaminski, N., Elias, J. A., Puchalski, J. T. & Takyar, S.. Lung Endothelial MicroRNA-1 Regulates Tumor Growth and Angiogenesis. Am J Respir Crit Care Med, 2017 Dec 1;196(11):1443-1455. PMID:28853613; PMCID: PMC5736970
- Korde A, Ahangari F, Haslip M, Zhang X, Liu Q, Cohn L, Gomez JL, Chupp G, Pober JS, Gonzalez A, Takyar S. An endothelial microRNA-1-regulated network controls eosinophil trafficking in asthma and chronic rhinosinusitis. The Journal of Allergy and Clinical Immunology 2020, 145:550-562.
2. The Role of Endothelium and VEGF in Lung Injury and Repair
We have studied the role of VEGF in three different contexts. (a) We studied the interaction of VEGF signaling and endothelial TLR4 in lung injury. We constructed vascular-specific lentiviral vectors and transgenic models to specifically manipulate TLR4 expression in the lung endothelium and found that endothelial TLR4 is required and sufficient for VEGF-mediated protection. A manuscript based on these findings was published in FASEB. (b) The role of RIG-like helicase (RLH): we found that processing of viral RNA mimics by RLH induces an interferon response in the lung and inhibits VEGF-induced angiogenesis. (c) Effect of VEGF on miRNA expression: we found that VEGF overexpression in the lung modulates the levels of 6 different microRNAs. I then showed that microRNA-1 downregulation occurs specifically in the lung endothelium and plays a critical role in VEGF-mediated angiogenesis. Our publications in this area include:
- Takyar S, Ahangari F, Lee CG, Elias JA. MicroRNA(MiR)-1 Regulates VEGF-induced Angiogenic Responses In The Lung By Inhibiting The Myeloproliferative Leukemia Virus Oncogene ( MPL). A59 Epigenetic of lung development and disease: American Thoracic Society; 2010. p. A2040-A2040
- Lee CG, Ma B, Takyar S, Ahangari F, Delacruz C, He CH, Elias JA. Studies of vascular endothelial growth factor in asthma and chronic obstructive pulmonary disease. Proc Am Thorac Soc 2011; 8: 512-515. PMID:22052929; PMCID:PMC3359071
- Ma B, Dela Cruz CS, Hartl D, Kang M-J, Takyar S, Homer RJ, Lee CG, Elias JA. RIG-like Helicase Innate Immunity Inhibits Vascular Endothelial Growth Factor Tissue Responses via a Type I IFN–dependent Mechanism. Am J Respir Crit Care Med 2012; 183: 1322-1335. PMC3114061
- Takyar S, Zhang Y, Haslip M, Jin L, Shan P, Zhang X, Lee PJ. An endothelial TLR4-VEGFR2 pathway mediates lung protection against oxidant-induced injury. FASEB 2016; 30(3):1317-27. PMID:26655705; PMCID:PMC4750407
3. The Role of Lung Cellular Repair Pathways in Asthma
We have worked in two areas in severe asthma. (a) Tissue Inhibitor of Metalloprotease-1 (TIMP-1) / Matrix Metalloprotease Proteins (MMP) pathway. We examined the role of proteases and their inhibitors in the development of Th2 inflammation and remodeling of the lung. I studied the pattern of gene expression in a TIMP-1 knockout mouse in Dr MF Sands’ lab. We showed that asthma phenotypes are accentuated in TIMP-1 knockout mouse and through quantitative methods showed that TIMP-1 has a critical role in inhibiting Th2-mediated inflammation and remodeling (b) Chitinase pathway: We studies the role of Chitinase 3 like 1 (Chi3L1) in obesity and asthma. We found that chitinases modulate both adipose tissue accumulation and airway hyperreactivity through regulation of Sirtuins. Our publications in this area include:
- Sands MF, Ohtake PJ, Mahajan SD, Takyar S, Aalinkeel R, Fang YV, Blume JW, Mullan BA, Sykes DE, Lachina S, Knight PR, Schwartz SA. Tissue inhibitor of metalloproteinase-1 modulates allergic lung inflammation in murine asthma. Clin Immunol 2009; 130: 186-198. PMID:18955015; PMCID:PMC2676334
- Ahangari F, Sood A, Ma B, Takyar S, Schuyler M, Qualls C, Dela Cruz CS, Chupp GL, Lee CG, Elias JA. Chitinase 3-like-1 regulates both visceral fat accumulation and asthma-like Th2 inflammation. Am J Respir Crit Care Med 2015; 191: 746-757. PMID:25629580; PMCID:PMC4407482
We have followed my molecular studies on miR-1 in several directions. Our studies on the role of miR-1 in tumor endothelium has led to the identification of a novel non-templated addition (NTA) enzymatic pathway. We also found that PI3 kinase/Akt pathway controls miR-1 levels in the endothelium. We presented these findings at the Keystone symposium on “MicroRNAs and Noncoding RNAs,” at the “Lung Development, Injury and Repair” Gordon Research Conference in 2016, at the ATS in 2016, 2017, and 2018. We have continued our studies on the role of miR-1 in the tumor stroma and found that it is regulated in the cancerization field. The preliminary results from these studies were presented at ATS 2018 and 2019.
Following the specific role of miR-1 in the endothelium, we used our vascular specific miRNA expression models to probe the specific roles of endothelial miR-1 in airway inflammation. We also developed an Argonaute 2 cross-linking and immunoprecipitation (Ago-CLIP) method to identify novel miR-1 targets through miRISC analysis. Using these two methods we showed that isolated overexpression of miR-1 in the lung endothelium significantly decreases the severity of airway inflammation and mediates this mechanism through downregulation of eosinophil trafficking genes. Also, through our collaboration with Yale Center for Asthma and Airway Disease (YCAAD), and the Ear Nose Throat Department at Yale, we showed the significance of this miRNA-regulated gene network in human asthma and chronic rhinosinusitis. These findings were published in Journal of Allergy and Clinical Immunology (JACI) in 2020.
We are currently pursuing a project on the protective role of miR-1 pathway in lung injury. We have shown that overexpression of miR-1 in the human and murine lung endothelium protects the lung against injury. These are recent observations in multiple ARDS murine models and human ex-vivo lung culture, and strongly suggest that miR-1 would be an effective treatment for SARS-CoV2-induced ARDS.
We collaborate with J.Steitz, Sterling Professor of Molecular Biophysics and Biochemistry and HHMI (Howard Hughes Medical Institute) at Yale on the molecular aspects of our projects, with Dr D. Boffa, Dr J. Puchalski and Dr M. Pisani at Thoracic Oncology Program (TOP), Thorciac Interventional Program, and Pulmonary and Critical Care section respectively, and with Dr Chupp and Dr Gomez at Yale Center for Asthma and Airway disease.
Asthma; Immunity, Cellular; Macrophage Activation; Neoplasms; Respiratory Distress Syndrome; Angiogenesis Inhibitors; MicroRNAs; Vascular Endothelial Growth Factor A